I expected to see a prompt where I can accept the certificate. Instead, I
get the "Unable to connect to a repository at URL ...' Server SSL
certificate verification failed: certificate issued for a different
hostname, issuer is not trusted" error.

I tried accepting the certificate permanently via terminal:
svn list <url>
I would then get "Authentication error"
What operating system are you using? What browser?
Ubuntu; Chrome

Recreating the issue for version 2.0.15, as there was no way to reopen the
issue #3317, whose status is fixed. I'm using PySVN.